MoleditPy-linux 4.3.2__tar.gz → 4.4.1__tar.gz

{moleditpy_linux-4.3.2 → moleditpy_linux-4.4.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 4.3.2
+Version: 4.4.1
 Summary: A cross-platform, simple, and intuitive molecular structure editor built in Python. It allows 2D molecular drawing and 3D structure visualization. It supports exporting structure files for input to DFT calculation software.
 Author-email: HiroYokoyama <titech.yoko.hiro@gmail.com>
 License:                     GNU GENERAL PUBLIC LICENSE
@@ -757,7 +757,7 @@ This application combines a modern GUI built with **PyQt6**, powerful cheminform
       * **Mirror:** Create a mirror image of the molecule across a selected plane (XY, XZ, or YZ).
       * **Set Bond Length, Angle, & Dihedral Angle:** Set precise numerical values for distances, angles, and torsional angles.
       * **Constrained Optimization:** Perform force field optimization (MMFF/UFF) while applying fixed constraints to specific distances, angles, or dihedral angles.
-  * **3D Measurement Tools:** A dedicated "Measure" mode allows you to click on atoms in the 3D view to instantly measure and display:
+  * **3D Measurement Tools:** The "Select" mode allows you to click on atoms in the 3D view to instantly measure and display:
       * **Distance** (between 2 atoms)
       * **Angle** (between 3 atoms)
       * **Dihedral Angle** (between 4 atoms)
@@ -893,7 +893,7 @@ Additionally, please cite the plugins you used.
       * **鏡像作成:** 選択した平面 (XY, XZ, YZ) に対して分子の鏡像を作成します。
       * **結合長・角度・二面角:** 原子を選択し、目標値を入力することで、距離、角度、ねじれ角を正確に設定します。
       * **制約付き最適化:** 特定の距離、角度、二面角を固定したまま、力場計算 (MMFF/UFF) による構造最適化を実行します。
-  * **3D測定ツール:** 専用の「Measure」モードで3Dビュー内の原子をクリックするだけで、以下の値を即座に測定・表示します。
+  * **3D測定ツール:** 「Select」モードで3Dビュー内の原子をクリックするだけで、以下の値を即座に測定・表示します。
       * **距離** (2原子間)
       * **角度** (3原子間)
       * **二面角** (4原子間)

{moleditpy_linux-4.3.2 → moleditpy_linux-4.4.1}/README.md

@@ -54,7 +54,7 @@ This application combines a modern GUI built with **PyQt6**, powerful cheminform
       * **Mirror:** Create a mirror image of the molecule across a selected plane (XY, XZ, or YZ).
       * **Set Bond Length, Angle, & Dihedral Angle:** Set precise numerical values for distances, angles, and torsional angles.
       * **Constrained Optimization:** Perform force field optimization (MMFF/UFF) while applying fixed constraints to specific distances, angles, or dihedral angles.
-  * **3D Measurement Tools:** A dedicated "Measure" mode allows you to click on atoms in the 3D view to instantly measure and display:
+  * **3D Measurement Tools:** The "Select" mode allows you to click on atoms in the 3D view to instantly measure and display:
       * **Distance** (between 2 atoms)
       * **Angle** (between 3 atoms)
       * **Dihedral Angle** (between 4 atoms)
@@ -190,7 +190,7 @@ Additionally, please cite the plugins you used.
       * **鏡像作成:** 選択した平面 (XY, XZ, YZ) に対して分子の鏡像を作成します。
       * **結合長・角度・二面角:** 原子を選択し、目標値を入力することで、距離、角度、ねじれ角を正確に設定します。
       * **制約付き最適化:** 特定の距離、角度、二面角を固定したまま、力場計算 (MMFF/UFF) による構造最適化を実行します。
-  * **3D測定ツール:** 専用の「Measure」モードで3Dビュー内の原子をクリックするだけで、以下の値を即座に測定・表示します。
+  * **3D測定ツール:** 「Select」モードで3Dビュー内の原子をクリックするだけで、以下の値を即座に測定・表示します。
       * **距離** (2原子間)
       * **角度** (3原子間)
       * **二面角** (4原子間)

{moleditpy_linux-4.3.2 → moleditpy_linux-4.4.1}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy-linux"
 
-version = "4.3.2"
+version = "4.4.1"
 
 license = {file = "LICENSE"}
 

{moleditpy_linux-4.3.2 → moleditpy_linux-4.4.1}/src/MoleditPy_linux.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 4.3.2
+Version: 4.4.1
 Summary: A cross-platform, simple, and intuitive molecular structure editor built in Python. It allows 2D molecular drawing and 3D structure visualization. It supports exporting structure files for input to DFT calculation software.
 Author-email: HiroYokoyama <titech.yoko.hiro@gmail.com>
 License:                     GNU GENERAL PUBLIC LICENSE
@@ -757,7 +757,7 @@ This application combines a modern GUI built with **PyQt6**, powerful cheminform
       * **Mirror:** Create a mirror image of the molecule across a selected plane (XY, XZ, or YZ).
       * **Set Bond Length, Angle, & Dihedral Angle:** Set precise numerical values for distances, angles, and torsional angles.
       * **Constrained Optimization:** Perform force field optimization (MMFF/UFF) while applying fixed constraints to specific distances, angles, or dihedral angles.
-  * **3D Measurement Tools:** A dedicated "Measure" mode allows you to click on atoms in the 3D view to instantly measure and display:
+  * **3D Measurement Tools:** The "Select" mode allows you to click on atoms in the 3D view to instantly measure and display:
       * **Distance** (between 2 atoms)
       * **Angle** (between 3 atoms)
       * **Dihedral Angle** (between 4 atoms)
@@ -893,7 +893,7 @@ Additionally, please cite the plugins you used.
       * **鏡像作成:** 選択した平面 (XY, XZ, YZ) に対して分子の鏡像を作成します。
       * **結合長・角度・二面角:** 原子を選択し、目標値を入力することで、距離、角度、ねじれ角を正確に設定します。
       * **制約付き最適化:** 特定の距離、角度、二面角を固定したまま、力場計算 (MMFF/UFF) による構造最適化を実行します。
-  * **3D測定ツール:** 専用の「Measure」モードで3Dビュー内の原子をクリックするだけで、以下の値を即座に測定・表示します。
+  * **3D測定ツール:** 「Select」モードで3Dビュー内の原子をクリックするだけで、以下の値を即座に測定・表示します。
       * **距離** (2原子間)
       * **角度** (3原子間)
       * **二面角** (4原子間)

{moleditpy_linux-4.3.2 → moleditpy_linux-4.4.1}/src/moleditpy_linux/ui/app_state.py

@@ -420,6 +420,19 @@ class StateManager:
                             # Skip property access if atom data is inconsistent
                             original_id = None
 
+                        # Implicit/explicit H counts raise on an unsanitized mol
+                        # (e.g. an XYZ import whose valences never passed
+                        # sanitization). Default to 0 so the structure still saves
+                        # and round-trips via the binary rather than being dropped.
+                        try:
+                            num_explicit_hs = atom.GetNumExplicitHs()
+                        except (RuntimeError, ValueError):
+                            num_explicit_hs = 0
+                        try:
+                            num_implicit_hs = atom.GetNumImplicitHs()
+                        except (RuntimeError, ValueError):
+                            num_implicit_hs = 0
+
                         atom_3d = {
                             "index": i,
                             "symbol": atom.GetSymbol(),
@@ -428,8 +441,8 @@ class StateManager:
                             "y": pos.y,
                             "z": pos.z,
                             "formal_charge": atom.GetFormalCharge(),
-                            "num_explicit_hs": atom.GetNumExplicitHs(),
-                            "num_implicit_hs": atom.GetNumImplicitHs(),
+                            "num_explicit_hs": num_explicit_hs,
+                            "num_implicit_hs": num_implicit_hs,
                             # include original editor atom id when available for round-trip
                             "original_id": original_id,
                         }
@@ -462,17 +475,21 @@ class StateManager:
                     "constraints_3d": json_safe_constraints,
                 }
 
-                # Molecular info
-                json_data["molecular_info"] = {
-                    "num_atoms": self.host.view_3d_manager.current_mol.GetNumAtoms(),
-                    "num_bonds": self.host.view_3d_manager.current_mol.GetNumBonds(),
-                    "molecular_weight": Descriptors.MolWt(
-                        self.host.view_3d_manager.current_mol
-                    ),
-                    "formula": rdMolDescriptors.CalcMolFormula(
-                        self.host.view_3d_manager.current_mol
-                    ),
-                }
+                # Molecular info — MolWt/CalcMolFormula can raise on an
+                # unsanitized mol; keep it optional so it never blocks the save.
+                try:
+                    json_data["molecular_info"] = {
+                        "num_atoms": self.host.view_3d_manager.current_mol.GetNumAtoms(),
+                        "num_bonds": self.host.view_3d_manager.current_mol.GetNumBonds(),
+                        "molecular_weight": Descriptors.MolWt(
+                            self.host.view_3d_manager.current_mol
+                        ),
+                        "formula": rdMolDescriptors.CalcMolFormula(
+                            self.host.view_3d_manager.current_mol
+                        ),
+                    }
+                except (AttributeError, RuntimeError, ValueError, TypeError) as e:
+                    logging.warning("Could not compute molecular info: %s", e)
 
                 # Identifiers (SMILES/InChI)
                 try:
@@ -637,7 +654,9 @@ class StateManager:
                                                 ValueError,
                                                 TypeError,
                                                 IndexError,
-                                            ):  # [RDKIT GUARD] RDKit atom property assignment may fail on invalid ids; skip silently.
+                                            ):
+                                                # [RDKIT GUARD] property set may
+                                                # fail on invalid ids; skip.
                                                 logging.debug(
                                                     "Suppressed non-critical error",
                                                     exc_info=True,

{moleditpy_linux-4.3.2 → moleditpy_linux-4.4.1}/src/moleditpy_linux/ui/compute_logic.py

@@ -455,7 +455,8 @@ class ComputeManager:
                 if item:
                     item.has_problem = True
                     item.update()
-        self.host.init_manager.view_2d.setFocus()
+        # Defer so Qt finishes routing the modal result before restoring focus.
+        QTimer.singleShot(0, self.host.init_manager.view_2d.setFocus)
 
     def _setup_mol_block_for_worker(self, mol: Chem.Mol) -> str:
         mol_block = self.host.state_manager.data.to_mol_block()
@@ -617,6 +618,9 @@ class ComputeManager:
         with suppress_log(TypeError, RuntimeError):
             QMessageBox.critical(self.host, "Calculation Error", msg)
 
+        # Restore 2D editor focus so keyboard shortcuts remain active.
+        QTimer.singleShot(0, self.host.init_manager.view_2d.setFocus)
+
     def create_atom_id_mapping(self) -> None:
         """Map 2D atom IDs to 3D RDKit indices."""
         if not self.host.view_3d_manager.current_mol:

{moleditpy_linux-4.3.2 → moleditpy_linux-4.4.1}/src/moleditpy_linux/ui/custom_interactor_style.py

@@ -25,6 +25,16 @@ from .atom_picking import pick_atom_index_from_screen
 
 from rdkit import Geometry
 
+# VTK's trackball state id for camera rotation (VTKIS_ROTATE); the enum is not
+# exposed to Python, so the literal is used with this name for clarity.
+_VTKIS_ROTATE = 1
+
+# Reference 3D-canvas size (px) that camera rotation speed is normalized to.
+# VTK's stock Rotate divides motion by the live render size, so rotation slows
+# as the canvas grows; normalizing to a fixed reference makes the speed
+# window-size independent and matches the feel at the default window size.
+_ROTATION_REFERENCE_SIZE = 640.0
+
 
 class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
     """VTK interactor style extending trackball-camera with 3D atom drag and measurement."""
@@ -81,6 +91,43 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
                 # Safe defensive fallback catching AttributeError, RuntimeError
                 logging.debug("Suppressed non-critical error", exc_info=True)
 
+    def _rotate_size_independent(self) -> None:
+        """Rotate the camera at a speed that does not depend on canvas size.
+
+        Mirrors vtkInteractorStyleTrackballCamera::Rotate but normalizes the
+        per-pixel azimuth/elevation to a fixed reference size instead of the
+        live render size, and scales by the user's rotation-sensitivity setting.
+        """
+        renderer = self.GetCurrentRenderer()
+        interactor = self.GetInteractor()
+        if renderer is None or interactor is None:
+            return
+
+        dx = interactor.GetEventPosition()[0] - interactor.GetLastEventPosition()[0]
+        dy = interactor.GetEventPosition()[1] - interactor.GetLastEventPosition()[1]
+
+        sensitivity = 1.0
+        mw = self.main_window
+        if mw is not None:
+            try:
+                sensitivity = float(
+                    mw.get_settings().get("mouse_rotation_sensitivity", 1.0)
+                )
+            except (AttributeError, TypeError, ValueError):
+                sensitivity = 1.0
+
+        delta = -20.0 / _ROTATION_REFERENCE_SIZE * self.GetMotionFactor() * sensitivity
+        camera = renderer.GetActiveCamera()
+        camera.Azimuth(dx * delta)
+        camera.Elevation(dy * delta)
+        camera.OrthogonalizeViewUp()
+
+        if self.GetAutoAdjustCameraClippingRange():
+            renderer.ResetCameraClippingRange()
+        if interactor.GetLightFollowCamera():
+            renderer.UpdateLightsGeometryToFollowCamera()
+        interactor.Render()
+
     def _stop_vtk_left_button_state(self) -> None:
         """Clear VTK's button/drag state after a custom-handled left click."""
         try:
@@ -501,8 +548,14 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
             # Custom atom drag
             self.is_dragging = True
         else:
-            # Delegate camera rotation to parent
-            super().OnMouseMove()
+            # Camera interaction. VTK's built-in Rotate divides mouse motion by
+            # the live render size, so rotation slows as the canvas grows. Handle
+            # the rotate state ourselves for window-size-independent speed;
+            # delegate pan/dolly/spin to the parent unchanged.
+            if self.GetState() == _VTKIS_ROTATE:
+                self._rotate_size_independent()
+            else:
+                super().OnMouseMove()
 
             # Update cursor display
             is_edit_active = (

{moleditpy_linux-4.3.2 → moleditpy_linux-4.4.1}/src/moleditpy_linux/ui/io_logic.py

@@ -35,7 +35,12 @@ from PyQt6.QtWidgets import (
 from rdkit import Chem
 from rdkit.Chem import AllChem, rdGeometry, rdMolTransforms, Descriptors
 
-from ..utils.constants import COVALENT_RADII, DUMMY_XYZ_SYMBOLS, VERSION
+from ..utils.constants import (
+    COVALENT_RADII,
+    DUMMY_XYZ_SYMBOLS,
+    VALID_ELEMENT_SYMBOLS,
+    VERSION,
+)
 
 
 class IOManager:
@@ -97,6 +102,38 @@ class IOManager:
         lines[3] = self.fix_mol_counts_line(lines[3])
         return "\n".join(lines)
 
+    @staticmethod
+    def _is_numeric_token(token: str) -> bool:
+        """True if *token* parses as a float."""
+        try:
+            float(token)
+            return True
+        except ValueError:
+            return False
+
+    @staticmethod
+    def _extract_xyz_coords(tokens: list[str]) -> Optional[Tuple[float, float, float]]:
+        """Return the first three float-parseable tokens as (x, y, z).
+
+        Skips non-numeric separator/label columns so ghost-atom rows like
+        ``XX : x y z`` (a colon in the second column) parse the same as a
+        standard ``symbol x y z`` row. Returns None if fewer than three numbers
+        are present.
+        """
+        nums: list[float] = []
+        for tok in tokens:
+            try:
+                nums.append(float(tok))
+            except ValueError:
+                if nums:
+                    break  # trailing non-numeric column after the coordinates
+                continue  # leading label/separator column before the coordinates
+            if len(nums) == 3:
+                break
+        if len(nums) == 3:
+            return (nums[0], nums[1], nums[2])
+        return None
+
     def _normalize_xyz_symbol(self, raw_symbol: str) -> Tuple[str, bool]:
         """Return the RDKit symbol for an XYZ atom and whether it is a dummy."""
         stripped = raw_symbol.strip()
@@ -105,11 +142,11 @@ class IOManager:
         if stripped.upper() in DUMMY_XYZ_SYMBOLS:
             return "*", True
         symbol = stripped.capitalize()
-        try:
-            atomic_num = Chem.GetPeriodicTable().GetAtomicNumber(symbol)
-        except (RuntimeError, ValueError, TypeError):
-            return "*", True
-        if atomic_num <= 0:
+        # Membership test rather than GetAtomicNumber(symbol): the latter makes
+        # RDKit's C++ layer print an "Element 'Xx' not found" violation to
+        # stderr for any dummy/pseudo label even though we catch the exception,
+        # which users read as a failed load.
+        if symbol not in VALID_ELEMENT_SYMBOLS:
             return "*", True
         return symbol, False
 
@@ -138,9 +175,19 @@ class IOManager:
 
         atoms_data = []
         has_dummy_atoms = False
-        atom_lines = lines[atom_start : atom_start + num_atoms]
+        nonstandard_rows = 0
+        atom_end = atom_start + num_atoms
+        atom_lines = lines[atom_start:atom_end]
         if len(atom_lines) < num_atoms:
-            raise ValueError("XYZ file format error: fewer atom rows than expected")
+            # Header count exceeds the rows present (truncated / miscounted file).
+            # Load the atoms that are actually there rather than refusing the
+            # whole file, so any parseable XYZ still opens.
+            logging.warning(
+                "XYZ declares %d atoms but only %d rows present; loading %d.",
+                num_atoms,
+                len(atom_lines),
+                len(atom_lines),
+            )
 
         for i, line in enumerate(atom_lines):
             parts = line.split()
@@ -149,9 +196,15 @@ class IOManager:
             raw_symbol = parts[0]
             symbol, is_dummy = self._normalize_xyz_symbol(raw_symbol)
             has_dummy_atoms = has_dummy_atoms or is_dummy
-            atoms_data.append(
-                (symbol, float(parts[1]), float(parts[2]), float(parts[3]))
-            )
+            coords = self._extract_xyz_coords(parts[1:])
+            if coords is None:
+                raise ValueError(f"Invalid atom data at line {atom_start + i + 1}")
+            # Standard rows put coordinates in the first three columns after the
+            # symbol; a non-numeric first column means an extra separator/label
+            # (e.g. the ':' in "XX : x y z") was skipped — flag it for the user.
+            if not self._is_numeric_token(parts[1]):
+                nonstandard_rows += 1
+            atoms_data.append((symbol, *coords))
 
         if not atoms_data:
             raise ValueError("No valid atoms found in XYZ file")
@@ -162,6 +215,8 @@ class IOManager:
             atom = Chem.Atom(symbol)
             atom.SetIntProp("xyz_unique_id", i)
             if atom.GetAtomicNum() == 0:
+                # Ghost/dummy rows (e.g. "XX : x y z") load as the wildcard "*";
+                # stash the real label token so it is kept for round-tripping.
                 atom.SetProp("xyz_original_symbol", atom_lines[i].split()[0])
             mol.AddAtom(atom)
             conf.SetAtomPosition(i, rdGeometry.Point3D(x, y, z))
@@ -190,7 +245,16 @@ class IOManager:
                 _set_prop(candidate, "_xyz_charge", charge_val)
                 return candidate
             else:
-                self.estimate_bonds_from_distances(mol)
+                # Distance-based bonding is best-effort: a failure here must not
+                # lose the molecule. The skip/dummy path only needs atoms and
+                # coordinates, so fall back to a bond-free structure so that any
+                # parseable XYZ still loads.
+                try:
+                    self.estimate_bonds_from_distances(mol)
+                except (RuntimeError, ValueError, TypeError, AttributeError) as e:
+                    logging.warning(
+                        "Bond estimation failed; loading atoms without bonds: %s", e
+                    )
                 candidate = mol.GetMol()
                 _set_prop(candidate, "_xyz_charge", charge_val)
                 return candidate
@@ -240,6 +304,8 @@ class IOManager:
 
         if final_mol:
             final_mol.xyz_atom_data = atoms_data
+            if nonstandard_rows:
+                _set_prop(final_mol, "_xyz_nonstandard_rows", nonstandard_rows)
         return final_mol
 
     def _report_load_error(self, title: str, message: str) -> None:
@@ -866,9 +932,17 @@ class IOManager:
             self.host.view_3d_manager.update_atom_id_menu_state()
 
             if self.host.statusBar():
-                self.host.statusBar().showMessage(
-                    f"3D Viewer Mode: Loaded {os.path.basename(file_path)}"
-                )
+                message = f"3D Viewer Mode: Loaded {os.path.basename(file_path)}"
+                nonstandard = 0
+                with suppress_log(AttributeError, KeyError, RuntimeError, TypeError):
+                    if mol.HasProp("_xyz_nonstandard_rows"):
+                        nonstandard = mol.GetIntProp("_xyz_nonstandard_rows")
+                if nonstandard:
+                    message += (
+                        f" (non-standard columns in {nonstandard} row(s); "
+                        "coordinates read from the numeric columns)"
+                    )
+                self.host.statusBar().showMessage(message)
             self.host.set_current_file_path(file_path)
             self.host.set_has_unsaved_changes(False)
             self.host.state_manager.update_window_title()

{moleditpy_linux-4.3.2 → moleditpy_linux-4.4.1}/src/moleditpy_linux/ui/molecular_scene_handler.py

@@ -426,11 +426,12 @@ class TemplateMixin:
         else:
             angle_step = 2 * math.pi / n
             start_angle = -math.pi / 2 if n % 2 != 0 else -math.pi / 2 - angle_step / 2
+            circumradius = bond_len / (2 * math.sin(math.pi / n))
             points = [
                 pos
                 + QPointF(
-                    bond_len * math.cos(start_angle + i * angle_step),
-                    bond_len * math.sin(start_angle + i * angle_step),
+                    circumradius * math.cos(start_angle + i * angle_step),
+                    circumradius * math.sin(start_angle + i * angle_step),
                 )
                 for i in range(n)
             ]

{moleditpy_linux-4.3.2 → moleditpy_linux-4.4.1}/src/moleditpy_linux/ui/settings_tabs/settings_3d_tabs.py

@@ -78,6 +78,16 @@ class Settings3DSceneTab(SettingsTabBase):
         self.projection_combo.addItems(["Perspective", "Orthographic"])
         form_layout.addRow("Projection Mode:", self.projection_combo)
 
+        # Camera rotation speed (0.10x–3.00x). Speed is normalized to a fixed
+        # reference canvas size, so it stays constant regardless of window size.
+        self.rotation_sens_slider, self.rotation_sens_label = self._create_slider(
+            10, 300, 100.0
+        )
+        form_layout.addRow(
+            "Mouse Rotation Speed:",
+            self._wrap_layout(self.rotation_sens_slider, self.rotation_sens_label),
+        )
+
     def _select_color(self) -> None:
         color = QColorDialog.getColor(QColor(self.current_bg_color), self)
         if color.isValid():
@@ -111,6 +121,9 @@ class Settings3DSceneTab(SettingsTabBase):
         if idx >= 0:
             self.projection_combo.setCurrentIndex(idx)
 
+        sens_val = settings_dict.get("mouse_rotation_sensitivity", 1.0)
+        self.rotation_sens_slider.setValue(int(sens_val * 100))
+
     def get_settings(self) -> dict[str, Any]:
         return {
             "background_color": self.current_bg_color,
@@ -120,6 +133,7 @@ class Settings3DSceneTab(SettingsTabBase):
             "specular": self.specular_slider.value() / 100.0,
             "specular_power": self.spec_power_slider.value(),
             "projection_mode": self.projection_combo.currentText(),
+            "mouse_rotation_sensitivity": self.rotation_sens_slider.value() / 100.0,
         }
 
 

{moleditpy_linux-4.3.2 → moleditpy_linux-4.4.1}/src/moleditpy_linux/utils/constants.py

@@ -24,7 +24,8 @@ def _get_version() -> str:
 
         try:
             return version("MoleditPy-linux")
-        except PackageNotFoundError:  # [OPTIONAL] Package not installed in editable mode; fall through to pyproject.toml.
+        except PackageNotFoundError:
+            # [OPTIONAL] Not installed in editable mode; fall through to pyproject.toml.
             logging.debug("Suppressed non-critical error", exc_info=True)
     except ImportError:
         logging.debug("Suppressed non-critical error", exc_info=True)
@@ -209,6 +210,13 @@ DEFAULT_CPK_COLORS = {
 
 
 pt = Chem.GetPeriodicTable()
+# Real element symbols (H..Og). Membership-test against this instead of calling
+# GetAtomicNumber() on an unknown label: probing the periodic table with a
+# non-element makes RDKit's C++ layer print an alarming "Element 'Xx' not found"
+# violation to stderr even when the Python exception is caught.
+VALID_ELEMENT_SYMBOLS: frozenset[str] = frozenset(
+    pt.GetElementSymbol(i) for i in range(1, 119)
+)
 # 0.3-scaled vdW radii for 3D display only — not physical values
 VDW_DISPLAY_RADII = {pt.GetElementSymbol(i): pt.GetRvdw(i) * 0.3 for i in range(1, 119)}
 # Deprecated alias kept for external plugins

{moleditpy_linux-4.3.2 → moleditpy_linux-4.4.1}/src/moleditpy_linux/utils/default_settings.py

@@ -19,6 +19,8 @@ DEFAULT_SETTINGS = {
     "specular_power": 20,
     "light_intensity": 1.0,
     "show_3d_axes": True,
+    # Camera rotation speed multiplier for the 3D scene (window-size independent).
+    "mouse_rotation_sensitivity": 1.0,
     # --- 3D Model Parameters (Ball and Stick) ---
     "ball_stick_atom_scale": 1.0,
     "ball_stick_bond_radius": 0.1,